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        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.

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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.25.1

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the nf-core/sarek analysis pipeline. For information about how to interpret these results, please see the documentation.

        Report generated on 2025-07-11, 12:43 CEST based on data in: /home/dolmom/Desktop/cnv_pipeline/work/12/939494e50a083f6d02898d7944d9b1

        General Statistics

        Showing 0/1 rows and 4/7 columns.
        Sample NameVarsSNPIndelTs/TvMNPMultiallelicMultiallelic SNP
        test_sample.manta.diploid_sv
        10306
        0
        5395
        0.00
        1
        0
        0

        Bcftools

        Utilities for variant calling and manipulating VCFs and BCFs.URL: https://samtools.github.io/bcftoolsDOI: 10.1093/gigascience/giab008

        Variant Substitution Types

        Variant Quality

        Created with MultiQC

        Indel Distribution

        Created with MultiQC

        Vcftools

        Program to analyse and reporting on VCF files.URL: https://vcftools.github.ioDOI: 10.1093/bioinformatics/btr330

        TsTv by Count

        Plot of TSTV-BY-COUNT - the transition to transversion ratio as a function of alternative allele count from the output of vcftools TsTv-by-count.

        Transition is a purine-to-purine or pyrimidine-to-pyrimidine point mutations. Transversion is a purine-to-pyrimidine or pyrimidine-to-purine point mutation. Alternative allele count is the number of alternative alleles at the site. Note: only bi-allelic SNPs are used (multi-allelic sites and INDELs are skipped.) Refer to Vcftools's manual (https://vcftools.github.io/man_latest.html) on --TsTv-by-count

        Created with MultiQC

        TsTv by Qual

        Plot of TSTV-BY-QUAL - the transition to transversion ratio as a function of SNP quality from the output of vcftools TsTv-by-qual.

        Transition is a purine-to-purine or pyrimidine-to-pyrimidine point mutations. Transversion is a purine-to-pyrimidine or pyrimidine-to-purine point mutation. Quality here is the Phred-scaled quality score as given in the QUAL column of VCF. Note: only bi-allelic SNPs are used (multi-allelic sites and INDELs are skipped.) Refer to Vcftools's manual (https://vcftools.github.io/man_latest.html) on --TsTv-by-qual

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        GroupSoftwareVersion
        BCFTOOLS_STATSbcftools1.2
        MANTA_GERMLINEmanta1.6.0
        VCFTOOLS_TSTV_COUNTvcftools0.1.16
        WorkflowNextflow25.04.6
        nf-core/sarekv3.5.1-g5fe5cdf

        nf-core/sarek Methods Description

        Suggested text and references to use when describing pipeline usage within the methods section of a publication.URL: https://github.com/nf-core/sarek

        Methods

        Data was processed using nf-core/sarek v3.5.1 (doi: 10.12688/f1000research.16665.2), (doi: 10.1093/nargab/lqae031), (doi: 10.5281/zenodo.3476425) of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

        The pipeline was executed with Nextflow v25.04.6 (Di Tommaso et al., 2017) with the following command:

        nextflow run nf-core/sarek -profile singularity -params-file params_PGP.yml

        References

        • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
        • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
        • Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
        • da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
        Notes:
        • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
        • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.

        nf-core/sarek Workflow Summary

        - this information is collected when the pipeline is started.URL: https://github.com/nf-core/sarek

        Input/output options

        input
        input/sample.csv
        outdir
        results/
        step
        variant_calling

        Main options

        intervals
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/intervals/wgs_calling_regions_noseconds.hg38.bed
        tools
        manta

        Variant Calling

        cf_chrom_len
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/Length/Homo_sapiens_assembly38.len
        pon
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz
        pon_tbi
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz.tbi

        Reference genome options

        ascat_alleles
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_alleles_hg38.zip
        ascat_genome
        hg38
        ascat_loci
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_loci_hg38.zip
        ascat_loci_gc
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/GC_G1000_hg38.zip
        ascat_loci_rt
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/RT_G1000_hg38.zip
        bwa
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex/
        bwamem2
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/BWAmem2Index/
        chr_dir
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/Chromosomes
        dbsnp
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz
        dbsnp_tbi
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi
        dbsnp_vqsr
        --resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_146.hg38.vcf.gz
        dict
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict
        dragmap
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/dragmap/
        fasta
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
        fasta_fai
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
        germline_resource
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz
        germline_resource_tbi
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz.tbi
        known_indels
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz
        known_indels_tbi
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi
        known_indels_vqsr
        --resource:gatk,known=false,training=true,truth=true,prior=10.0 Homo_sapiens_assembly38.known_indels.vcf.gz --resource:mills,known=false,training=true,truth=true,prior=10.0 Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
        known_snps
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz
        known_snps_tbi
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz.tbi
        known_snps_vqsr
        --resource:1000G,known=false,training=true,truth=true,prior=10.0 1000G_omni2.5.hg38.vcf.gz
        mappability
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/Control-FREEC/out100m2_hg38.gem
        ngscheckmate_bed
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/NGSCheckMate/SNP_GRCh38_hg38_wChr.bed
        sentieon_dnascope_model
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model
        snpeff_db
        GRCh38.105
        vep_cache_version
        113
        vep_genome
        GRCh38
        vep_species
        homo_sapiens

        Core Nextflow options

        configFiles
        /home/dolmom/.nextflow/assets/nf-core/sarek/nextflow.config
        containerEngine
        singularity
        launchDir
        /home/dolmom/Desktop/cnv_pipeline
        profile
        singularity
        projectDir
        /home/dolmom/.nextflow/assets/nf-core/sarek
        revision
        master
        runName
        prickly_raman
        userName
        dolmom
        workDir
        /home/dolmom/Desktop/cnv_pipeline/work

        MultiQC v1.25.1 - Written by Phil Ewels, available on GitHub.

        This report uses Plotly, jQuery, jQuery UI, Bootstrap and FileSaver.js.